Using our allele-specific PCR assay, which allows detection and quantification of rare mutations at levels as low as 0.1% in a virus population, we are performing studies designed to understand the dynamics of appearance and disappearance of NNRTI resistance mutations in patients starting and stopping therapy as well as in drug-naive patients. In collaboration with Dr. Mellors, we are assessing the impact of low-frequency mutations on subsequent treatment failure. In collaboration with Drs. Lynn Morris (South Africa) and Pat Robertson (Boehringer Ingelheim), we are also analyzing the rise and fall of NNRTI resistance mutations in women exposed to single-dose nevirapine to prevent mother-to-infant transmission, and to assess the consequences of these mutations for subsequent nevirapine-based therapy. The assay is also being used for collaborative studies with DRP investigators. With Dr. Vineet Kewalramani, we are assessing the appearance of NNRTI resistance mutations in a pigtail macaque model of infection with SIV containing HIV RT (RT-SHIV) and treated with efavirenz, as a model for the evolution of resistance in humans so treated. In collaboration with Dr. Eric Freed, we are developing a sensitive assay for the duplication of the PTAP motif in the p6 portion of Gag frequently found in association with drug resistance.